By Jacqueline A. Odgis
Scientific Program Analyst, NHGRI

Cost-effective, high throughput technologies used to analyze DNA are uncovering variations in our genetic code. Increasing numbers of these variations, sometimes referred to as mutations, are implicated in disease, including many cancers. With the ability to sequence DNA in the clinic, doctors can more definitively diagnose and predict patients' personal risks for developing cancer, based on the presence of these variants in their DNA.

For some types of cancer, the damaging variations are inherited. Thus, our parents' medical history might provide clues to disease risks to look for in ourselves. However, there are other types of changes that increase cancer risk that form in our cells after birth, before symptoms appear.

The question then is, how do we seek out those individuals who may be at higher risk, but have no history of cancer in their family? To help solve this problem, scientists are investigating "pre-cancerous" mutations that might allow us to catch, monitor and possibly treat cancer caught early in otherwise healthy patients.

The December Genome Advance of the Month explores the use of specific genetic mutations to identify patients at high risk for cancer, even in people without a family history of the disease. The research team, led by Giulio Genovese, Ph.D., of the Broad Institute at MIT and Harvard in Boston, focused on precursors for blood cancers like leukemia, lymphoma and myeloma. Though innovative drug therapies and increasing access to treatments have dramatically improved blood cancer survival, blood cancer remains one of the most common forms of cancer in the United States and worldwide. In 2014, blood cancer accounted for approximately 9.4 percent of the estimated 1,665,540 new cancer cases diagnosed across the country.

Turning to the human genome for clues, Dr. Genovese and his group looked closely at tiny fragments of DNA that float in the blood stream to observe the dynamics of stem cells - unspecialized cells from which many different cell types arise. In a process called "clonal expansion," stem cells divide to create copies of themselves, each copy containing the same DNA as the original stem cell. In this way, if the stem cell's DNA contains mutations at specific sites in the sequence, then this same sequence - mutations and all - will be inherited by their clones.

Dr. Genovese's team used blood samples from 12,380 patients enrolled in the Swedish National Patient Register to assess what mutations, if any, existed in the sample cells' DNA. They then compared the proportion of a patient's normal DNA to the proportion with mutations. (Patient's normal DNA and the DNA with mutations were suspended in the same blood sample.) The normal DNA appeared in higher proportions than that of the DNA with mutations. If researchers discovered a significant proportion of DNA with the same mutations, this indicated that a clonal expansion had occurred.

Researchers then reviewed 11,164 participants' medical records from 1965-2012 to see if any specific mutations were common among other patients who had similar health histories. They followed the health outcomes of these patients for two to seven years after the initial blood draw and noted, for the purposes of this study, if any of them had developed blood cancer since the time of the sampling.

In comparing all patients' DNA sequences, mutations that had undergone proliferation through clonal expansion were most frequently found in four genes - DNMT3A, ASXL1, TET2 and PPM1D. All of these gene mutations had previously been associated with blood cancer. Interestingly, mutations in these genes were not shown to be cancerous in and of themselves; instead, they increased the susceptibility of cells to develop cancer-causing mutations later on, in other regions of the genome. In this way, they acted as a "driver" of blood-born cancer.

Overall, a number of risk factors were found to be associated with blood cancer. First, patients found to have driver mutations were more likely to develop blood cancer than those without them. The number of clones with the mutations within the blood sample was also identified as a strong risk factor for blood cancer. About 42 percent of patients diagnosed with blood cancer more than six months after blood sampling were found to have elevated levels of mutated DNA.

Although clonal expansion of mutations was shown to confer a high risk of blood cancer, it was detected in about 10 percent of elderly patients and only 0.7 percent of patients younger than 50 years. For each year following the initial detection, the risk of developing blood cancer increased 1.0 percent. Therefore, the risk is relatively low and may not warrant the patient receiving knowledge of this increased risk, considering the potential emotional impact and the limitations of intervention options in this pre-clinical stage.

From this study, we can see how DNA sequencing techniques can be applied to assess blood cancer risk in pre-symptomatic people. The opportunity to detect cancer in a pre-clinical state is promising as the mutations studied were not likely to be inherited at birth.

It will be exciting to see the results of further investigations on the effect of combinations of mutations in DNMT3A, ASXL1, TET2 and PPM1D and other genes. Closer examination of these genes' functions might also provide insight into how these mutations influence the onset, progression and severity of different blood cancers. DNA sequencing, used in this way, shows promise as a tool to identify cancer risk variations, which ultimately could serve as life-saving pre-clinical indicators of blood cancer and other diseases.